Class/Object

nl.biopet.tools.vcffilter

Args

Related Docs: object Args | package vcffilter

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case class Args(inputVcf: File = null, outputVcf: File = null, invertedOutputVcf: Option[File] = None, minQualScore: Option[Double] = None, minSampleDepth: Int = 1, minTotalDepth: Int = 1, minAlternateDepth: Int = 1, minSamplesPass: Int = 1, mustHaveVariant: List[String] = Nil, mustNotHaveVariant: List[String] = Nil, calledIn: List[String] = Nil, mustHaveGenotype: List[(String, GenotypeType)] = Nil, uniqueVariantInSample: String = null, resToDom: List[Trio] = Nil, trioCompound: List[Trio] = Nil, deNovoTrio: List[Trio] = Nil, trioLossOfHet: List[Trio] = Nil, booleanArgs: BooleanArgs = Args.BooleanArgs(), diffGenotype: List[(String, String)] = Nil, filterHetVarToHomVar: List[(String, String)] = Nil, iDset: Set[String] = Set(), minGenomeQuality: Int = 0, advancedGroups: List[List[String]] = Nil, minCalled: Int = 0) extends Product with Serializable

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Serializable, Serializable, Product, Equals, AnyRef, Any
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Instance Constructors

  1. new Args(inputVcf: File = null, outputVcf: File = null, invertedOutputVcf: Option[File] = None, minQualScore: Option[Double] = None, minSampleDepth: Int = 1, minTotalDepth: Int = 1, minAlternateDepth: Int = 1, minSamplesPass: Int = 1, mustHaveVariant: List[String] = Nil, mustNotHaveVariant: List[String] = Nil, calledIn: List[String] = Nil, mustHaveGenotype: List[(String, GenotypeType)] = Nil, uniqueVariantInSample: String = null, resToDom: List[Trio] = Nil, trioCompound: List[Trio] = Nil, deNovoTrio: List[Trio] = Nil, trioLossOfHet: List[Trio] = Nil, booleanArgs: BooleanArgs = Args.BooleanArgs(), diffGenotype: List[(String, String)] = Nil, filterHetVarToHomVar: List[(String, String)] = Nil, iDset: Set[String] = Set(), minGenomeQuality: Int = 0, advancedGroups: List[List[String]] = Nil, minCalled: Int = 0)

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. val advancedGroups: List[List[String]]

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  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  6. val booleanArgs: BooleanArgs

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  7. val calledIn: List[String]

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  8. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  9. val deNovoTrio: List[Trio]

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  10. val diffGenotype: List[(String, String)]

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  11. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  12. val filterHetVarToHomVar: List[(String, String)]

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  13. def finalize(): Unit

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    protected[java.lang]
    Definition Classes
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    @throws( classOf[java.lang.Throwable] )

  14. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  15. val iDset: Set[String]

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  16. val inputVcf: File

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  17. val invertedOutputVcf: Option[File]

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  18. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  19. val minAlternateDepth: Int

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  20. val minCalled: Int

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  21. val minGenomeQuality: Int

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  22. val minQualScore: Option[Double]

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  23. val minSampleDepth: Int

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  24. val minSamplesPass: Int

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  25. val minTotalDepth: Int

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  26. val mustHaveGenotype: List[(String, GenotypeType)]

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  27. val mustHaveVariant: List[String]

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  28. val mustNotHaveVariant: List[String]

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  29. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  30. final def notify(): Unit

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    Definition Classes
    AnyRef

  31. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  32. val outputVcf: File

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  33. val resToDom: List[Trio]

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  34. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  35. val trioCompound: List[Trio]

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  36. val trioLossOfHet: List[Trio]

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  37. val uniqueVariantInSample: String

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  38. final def wait(): Unit

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    Definition Classes
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    Annotations
    @throws( ... )

  39. final def wait(arg0: Long, arg1: Int): Unit

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    @throws( ... )

  40. final def wait(arg0: Long): Unit

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    Definition Classes
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    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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